image/svg+xml (Hernández & Gómez-Hinostrosa, 2015) - Mammillaria is distributed from the southern United States to Central America. - Mexico is the center of diversity for the genus - The number of recognized species varies on the author: Reppenhagen (1992) considered 320 spp; Pilbeam (1999) 181 spp and Hunt (2006) 163 spp. Its name derived from Latin mammilla, "nipple", referring to tubercles. https://github.com/cristoichkov/GBS_Bioinf_Process_Mamm Changes circumscription of M. haageana according to some taxonomic proposals. Distribution of M. haageana M. haageana subsp. haageana M. haageana subsp. meissneri M. haageana subsp. meissneri M. haageana subsp. conspicua M. haageana subsp. conspicua M. haageana subsp. conspicua M. haageana subsp. acultzingensis M. haageana subsp. san- angelensis clust_threshold.-This the level of sequence similarity at which two sequences are identified as being homologous, and thuscluster together. mindepth_majrul.- This is the minimum depth at which majority rule base calls are made during step 5 consensus base calling. Not recommend using values higher than 0.95, as homologous sequences may not cluster together at such high threshold due to the presence of Ns, indels, sequencing errors, or polymorphisms (Eaton, 2015). ++ Grupo externo Grupo Interno M. albilanata ssp. oaxacana Mao_1 Mao_4 Mao_5 Mao_3 M. haageana Mhsa Mhm_1 Mhm_1 Mhm_3 Mhc_8 Mhc_7 Mhh_3 Mhc_5 Mhh_2 Mha_1 Mhh_1 Phylogenetic tree generated with RAxML of 125 taxa based on two chloroplast markers (rpl16 and psbA-trnH), bootstrap support values are shown. The concatenated matrix follows a model of molecular evolution TVM + I + G Mammillaria zephyranthoides Bravo-Hollis and Sánchez- Mejorada (1991) Pilbeam (1999) Reppenhagen (1992) Guzmán (2003) Hunt (2006) M. haageana M. haageana M. haageana M. haageana M. haageana M. vaupelii ssp. haageana M. meissneri ssp. haageana M. collina ssp. conspicua M. donatii ssp. acultzingensis M. donati ssp. elegans M. conspicua ssp. conspicua M. san-angelensis ssp. san-angelensis var. vaupelii ssp. elegans M. conspicua ssp. schmollii M. albidula ssp. meissneri ssp. acultzingensis M. elegans ssp. san-angelensis var. lupina ssp. vaupelii var. longicaudata var. teyuca M. haageana subsp. san- angelensis M. haageana subsp. acultzingensis M. haageana subsp. meissneri M. haageana subsp. conspicua M. haageana subsp. haageana Escobaria_chihuahuensis Pelecyphora_aselliformis Coryphantha_pallida Coryphantha_durangensis Escobaria_zilziana Coryphantha_hesteri Coryphantha_vivipara M_wrightii M_barbata M_luethyi Neolloydia_conoidea Ortegocactus_macdougallii M_tetrancistra M_guelzowiana M_boolii M_schumannii M_pondii M_halei M_poselgeri M_oteroi M_zephyranthoides M_beneckei M_sphacelata M_herrerae M_humboldtii M_candida M_senilis M_weingartiana M_longimamma M_moelleriana M_hernandezii M_pottsii M_pectinifera M_picta M_prolifera M_glassii M_plumosa M_bombycina M_perezdelarosae M_decipiens M_elongata M_microhelia M_vetula_subsp_gracilis M_melanocentra_subsp_rubrograndis M_grusonii M_mammillaris M_magnimamma M_lindsayi M_peninsularis M_rhodantha M_huitzilopochtlii_ssp_huitzilopochtlii M_huitzilopochtlii_ssp_niduliformis M_crucigera_tlalocii M_crucigera_ssp_crucigera M_albilanata_ssp_oaxacana_CC036 M_lanata M_eriacantha M_columbiana_ssp_columbiana M_columbiana_ssp_yucatanensis M_albilanata_ssp_oaxacana_CC044 M_haageana_CC024 M_haageana_CDMX M_albilanata_ssp_oaxacana_CC046 M_haageana_CC023 M_haageana_CC025 M_haageana_CC027 M_dixanthocentron M_supertextae M_haageana_CC045 M_albilanata_ssp_reppenhagenii M_albilanata_ssp_tegelbergiana M_albilanata_ssp_albilanata M_haageana_CC039 M_albilanata_ssp_oaxacana_CC040 M_favicentra M_haageana_CC022 M_haageana_CC035 M_haageana_CC021 M_haageana_CC029 M_haageana_CC020 Ser. Polyacanthae Ser. Leucocephalae Ser. Polyedrae Ser. Lasiacanthae subg. Chilita Outgroup 100 22 28 58 87 82 100 100 99 52 93 76 89 94 90 44 59 42 98 58 83 90 33 52 60 52 53 4 17 14 34 43 100 100 72 42 54 83 37 24 11 92 39 67 87 91 79 83 40 54 65 36 23 65 87 30 41 27 clade S1 clade S2 clade S3 clade S4 Morphological variation in M. haageana Phylogenetic analysis to know the position of M. haageana Selected samples and plate design for sequencing using GBS Bioinformatic workflow 97.2% 2.79% 94.74% 5.25% 95.41% 4.58% 0 25 50 75 100 GBSXipyradStacks Demultiplex software Percentage % No_match_reads Match_reads 6e+06 4e+06 2e+06 1e+06 8e+05 Samples Number of reads Species M_albilanata_albilanta M_albilanata_oaxacana M_albilanata_reppenhagenii M_crucigera M_dixanthocentron M_duoformis M_flavicentra M_haageana_acultzingensis M_haageana_conspicua M_haageana_haageana M_haageana_meissneri M_haageana_san_angelensis M_huitzilopochtli M_lanata M_magnimamma M_myxtax M_supertexta 20000 40000 60000 0.820.850.880.910.94 Clust threshold Number of SNPs min_sam_loc 40% 60% 80% 1000 2000 3000 4000 0.820.850.880.910.94 Clust threshold Number of loci min_sam_loc 40% 60% 80% 25000 50000 75000 100000 3456 Mindepth majrule Number of SNPs min_sam_loc 40% 60% 80% 1000 2000 3000 4000 3456 Mindepth majrule Number of loci min_sam_loc 40% 60% 80% −75 −50 −25 0 25 0.82/0.850.85/0.880.88/0.910.91/0.94 Iteration of clust threshold Number of new Loci DGDC-REPSA-PAPIME-PAPIIT Acknowledgment Comparison between three software Number of reads per sample Plots of iterating values of the level of sequence similarity Plots of iterating values the minimum depth Plots of the number of new loci Not recommend using values higher than 0.95, as homologous sequences may not cluster together at such high threshold due to the presence of Ns, indels, sequencing errors, or polymorphisms (Eaton, 2015). ++ This Figure describes how increasing values for clust_threshold contributed new broadly shared, and therefore likely real loci.
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